I can see from the saddle positions that the three high strings are not intonated - the saddles are hard against the back of the bridge, and are not showing the same diagonal line as the lower strings - they should have that diagonal. The bridge is mounted too far forwards. I believe you can get studs which have a kind of joggle where they emerge from the body. This allows the bridge to sit in a different position. In your case it needs to move back. An alternative solution would be a bridge with a wider range of travel for the saddles. Not sure what this would be but someone will know.